nextflow.config

manifest {
    nextflowVersion = '!>=23.04.0'
    mainScript = "main.nf"
}

plugins {
  id 'nf-validation'
}

params {

    dbs = "databases"
    // Used to store files and workdir
    project                    = ""
    metagenome                 = ""
    biomes                     = ""

    // Input
    samplesheet                = ""
    assembly_software_file     = ""
    
    // Feature flags
    skip_preprocessing_input   = false
    merge_pairs                = false
    skip_prok                  = false
    skip_euk                   = false

    skip_maxbin2               = false
    skip_metabat2              = false
    skip_concoct               = false

    min_contig_size            = 1500
    metabat2_rng_seed          = 1

    // Reference databases
    // Defaults only, expecting to be overwritten
    busco_db                   = "/path/to/busco-db"
   
    // change to corresponding release
    cat_db_folder              = "/path"
    cat_diamond_db             = "/path/to/diamond"
    cat_taxonomy_db            = "2021-01-07_taxonomy"

    checkm2_db                 = "/path/to/uniref100.KO.1.dmnd"

    eukcc_db                   = "/path/to/eukccdb/eukcc2_db_ver_1.2"
    gunc_db                    = "/path/to/gunc_db_2.0.4.dmnd"
    gtdbtk_db                  = "/path/to/release207_v2"

    ref_genome                 = "/path/to/bwa-mem2-hg38.fa"
    rfam_rrna_models           = "/path/to/rfams_cms"

    gtdbtk_db                  = "/path/to/gtdbtk_ref_db"

    // dRep Euks args
    euk_drep_args              = "-pa 0.80 -sa 0.99 -nc 0.40 -cm larger -comp 49 -con 21"
    euk_drep_args_mags         = "-pa 0.80 -sa 0.95 -nc 0.40 -cm larger -comp 49 -con 21"

    // MultiQC options
    multiqc_config             = null
    multiqc_title              = null
    multiqc_logo               = null
    multiqc_methods_description = null

    // Boilerplate options
    outdir                     = null
    publish_dir_mode           = 'copy'
    help                       = false
    version                    = false

    // Max resource options
    // Defaults only, expecting to be overwritten
    max_memory                 = '128.GB'
    max_cpus                   = 16
    max_time                   = '240.h'

    // Schema validation default options
    validationFailUnrecognisedParams = false
    validationLenientMode            = false
    validationSchemaIgnoreParams     = ''
    validationShowHiddenParams       = false
    validate_params                  = true
}

includeConfig 'config/dbs.config'
includeConfig 'config/base.config'
includeConfig 'config/codon.config'
includeConfig 'config/modules.config'

profiles {
    singularity {
       enabled = true
       autoMounts = true
       cacheDir = params.singularity_cachedir
       registry = 'quay.io'
    }

    lsf {
        workDir = params.workdir
        params.databases = params.dbs
        executor {
            name = "lsf"
            queueSize = 200
        }
        params.cloudProcess = true
        process.cache = "lenient"
    }

    slurm {
        workDir = params.workdir
        params.databases = params.dbs
        executor {
            name = "slurm"
            queueSize = 200
        }
        params.cloudProcess = true
        process.cache = "lenient"
    }

    local {
         docker {
            enabled = true
            autoMounts = true
            registry = 'quay.io'
            userEmulation = true
            runOptions = "--platform linux/x86_64"
        }
        executor {
            name = "local"
            cpus = 2
            memory = '1 GB'
        }
    }
}

// Set default registry for Apptainer, Docker, Podman and Singularity independent of -profile
apptainer.registry   = 'quay.io'
docker.registry      = 'quay.io'
podman.registry      = 'quay.io'

// Export these variables to prevent local Python/R libraries from conflicting with those in the container
// The JULIA depot path has been adjusted to a fixed path `/usr/local/share/julia` that needs to be used for packages in the container.
// See https://apeltzer.github.io/post/03-julia-lang-nextflow/ for details on that. Once we have a common agreement on where to keep Julia packages, this is adjustable.

env {
    PYTHONNOUSERSITE = 1
    R_PROFILE_USER   = "/.Rprofile"
    R_ENVIRON_USER   = "/.Renviron"
    JULIA_DEPOT_PATH = "/usr/local/share/julia"
}

// Capture exit codes from upstream processes when piping
process.shell = ['/bin/bash', '-euo', 'pipefail']

def trace_timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')
timeline {
    enabled = true
    file    = "${params.outdir}/pipeline_info/execution_timeline_${trace_timestamp}.html"
}
report {
    enabled = true
    file    = "${params.outdir}/pipeline_info/execution_report_${trace_timestamp}.html"
}
trace {
    enabled = true
    file    = "${params.outdir}/pipeline_info/execution_trace_${trace_timestamp}.txt"
}
dag {
    enabled = true
    file    = "${params.outdir}/pipeline_info/pipeline_dag_${trace_timestamp}.html"
}

manifest {
    name            = 'ebi-metagenomics/genomes-generation'
    author          = """Microbiome Informatics team"""
    homePage        = 'https://github.com/ebi-metagenomics/genomes-generation'
    description     = """Microbiome Informatics MAGs generation pipeline"""
    mainScript      = 'main.nf'
    nextflowVersion = '!>=23.04.0'
    version         = '1.0dev'
    doi             = ''
}

def check_max(obj, type) {
    if (type == 'memory') {
        try {
            if (obj.compareTo(params.max_memory as nextflow.util.MemoryUnit) == 1)
                return params.max_memory as nextflow.util.MemoryUnit
            else
                return obj
        } catch (all) {
            println "   ### ERROR ###   Max memory '${params.max_memory}' is not valid! Using default value: $obj"
            return obj
        }
    } else if (type == 'time') {
        try {
            if (obj.compareTo(params.max_time as nextflow.util.Duration) == 1)
                return params.max_time as nextflow.util.Duration
            else
                return obj
        } catch (all) {
            println "   ### ERROR ###   Max time '${params.max_time}' is not valid! Using default value: $obj"
            return obj
        }
    } else if (type == 'cpus') {
        try {
            return Math.min( obj, params.max_cpus as int )
        } catch (all) {
            println "   ### ERROR ###   Max cpus '${params.max_cpus}' is not valid! Using default value: $obj"
            return obj
        }
    }
}